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RTXteam / RTX-KG2

Build system for the RTX-KG2 biomedical knowledge graph, part of the ARAX reasoning system (https://github.com/RTXTeam/RTX)
MIT License
39 stars 8 forks source link

RepoDB Conversion Script Fails #298

Closed ecwood closed 1 year ago

ecwood commented 1 year ago

While testing for https://github.com/RTXteam/RTX-KG2/issues/296, I found that repodb_csv_to_kg_json.py fails:

/home/ubuntu/kg2-venv/lib/python3.7/site-packages/rdflib_jsonld/__init__.py:12: DeprecationWarning: The rdflib-jsonld package has been integrated into rdflib as of rdflib==6.0.0.  Please remove rdflib-jsonld from your project's dependencies.
  DeprecationWarning,
Traceback (most recent call last):
  File "repodb_csv_to_kg_json.py", line 75, in <module>
    graph = make_kg2_graph(input_file_name, test_mode)
  File "repodb_csv_to_kg_json.py", line 43, in make_kg2_graph
    knowledge_source=REPODB_CURIE + ':')]
TypeError: make_node() got an unexpected keyword argument 'knowledge_source'

Also note, our CSV of this source hasn't been updated since October 2019. We might want to examine whether this is still a valuable source since it is so outdated.

ecwood commented 1 year ago

I am closing this issue because the code worked in KG2.8.4pre's build.